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báo cáo khoa học: " An overview of the Phalaenopsis orchid genome through BAC end sequence analysis"

Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành y học dành cho các bạn tham khảo đề tài: An overview of the Phalaenopsis orchid genome through BAC end sequence analysis | Hsu et al. BMC Plant Biology 2011 11 3 http www.biomedcentral.eom 1471-2229 11 3 BMC Plant Biology RESEARCH ARTICLE Open Access An overview of the Phalaenopsis orchid genome through BAC end sequence analysis 1 1 1 1 1 2 3 1 Chia-Chi Hsu Yu-Lin Chung Tien-Chih Chen Yu-Ling Lee Yi-Tzu Kuo Wen-Chieh Tsai Yu-Yun Hsiao Yun-Wen Chen1 Wen-Luan Wu1 2 3 Hong-Hwa Chen1 2 3 Abstract Background Phalaenopsis orchids are popular floral crops and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome BAC end sequences BESs can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding. Results We used two BAC libraries constructed using the BamHI and HindIII restriction enzymes of Phalaenopsis equestris to generate pair-end sequences from 2 920 BAC clones 71.4 and 28.6 from the BamHI and HindIII libraries respectively at a success rate of 95.7 . A total of 5 535 BESs were generated representing 4.5 Mb or about 0.3 of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1 397 base pairs bp in size with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches it was found that 641 11.6 were predicted to represent protein-encoding regions whereas 1 272 23.0 contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons 41.9 and 12.8 respectively whereas only 10.8 were DNA transposons. Further 950 potential simple sequence repeats SSRs were discovered. Dinucleotides were the most abundant repeat motifs AT TA dimer repeats were the most frequent SSRs representing 253 26.6 of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis and even fewer mapped to the rice genome. .